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F Feltus

Associate Professor
Genetics and Biochemistry Department

Office: 302C Biosystems Research Complex, C
Phone: 864-656-3231
Email: ffeltus@clemson.edu
Vita: Download CV
Personal Website: https://www.linkedin.com/pub/alex-feltus/3a/7/86a

 

 Educational Background

Ph.D. Cell Biology
Vanderbilt University 2000

B.Sc. Biochemistry
Auburn University 1992

 Courses Taught

Bioinformatics
Computational Genomics
Biomedical Informatics
Intro. to Next-Generation Sequence Analysis Workflows Workshop
Special Topics in Advanced Biochemistry and Genetics (Network and Systems Genetics)
Essential Elements of Biochemistry
Issues in Research
Senior Seminar
Perl for Bioinformatics

 Profile

Dr. F. Alex Feltus received a B.Sc. in Biochemistry from Auburn University in 1992, served two years in the Peace Corps, and then completed advanced training in biomedical sciences at Vanderbilt and Emory. Since 2002, he has performed research in bioinformatics, high-performance computing, cyberinfrastructure, network biology, genome assembly, systems genetics, paleogenomics, and bioenergy feedstock genetics. Currently, Feltus is an Associate Professor in Clemson University’s Dept. of Genetics & Biochemistry and CEO of Allele Systems LLC. Feltus has published numerous scientific articles in peer-reviewed journals, teaches undergrad and PhD students in bioinformatics, biochemistry, and genetics. At present, he is funded by multiple NSF grants and is engaged in tethering together extremely smart people from diverse technical backgrounds in an effort to propel genomics research from the Excel-scale towards the Exascale.

 Research Interests

Systems Genetics. The Feltus lab is discovering causal gene sets underlying complex trait expression ranging from the control of bioenergy feedstock traits to root nodulation to autism spectrum disorders to intersecting pathways in various tumor states. Gene sets are discovered de novo with high performance computing and network biology techniques. With networks, we embrace biological complexity and measure, model and interpret gene expression relationships and gene product physical interactions on a massive scale. At our core, we build, integrate, and interpret gene co-expression networks to reveal functionally-related genes based upon the simultaneous co-expression of gene pairs across hundreds to thousands of gene expression profiling experiments (microarray, RNAseq). By combining high-throughput construction of co-expression networks with additional biological data, we are discovering and validating genetic subsystems in plants and animals controlling specific biochemical pathways and quantitative phenotypes.

Our lab has been especially interested in advancing the field of systems genetics in grasses centered on rice and sorghum, and we are exploring how gene networks have been modified to meet the physiological requirements of a particular species through comparative network analysis between grasses. Recently, the Feltus lab has been applying these techniques to vertebrates with a translational bioinformatics slant toward tumor biomarker module discovery using The Cancer Genome Atlas, public human RNAseq data, and private data from a breast cancer redirection model in collaboration with Brian Booth at Clemson. For data mining purposes, we have created a Tripal-based system genetics module explorer (GeneNetEngine; sysbio.genome.clemson.edu) for digging into biological networks. Funding support: "PGRP: Spatial and Temporal Resolution of mRNA Profiles During Early Nodule Development" (NSF-PGRP, $1,932,798); "Genomic and Breeding Foundations for Bioenergy Sorghum Hybrids" (USDA-DOE: DE-FOA-000041, $1,200,000).

Big Data Bioinformatics and Cyberinfrastructure. As genomics enters the Big Data scale, data transfer, storage and analysis will all become more difficult. Fortunately, there are many low hanging fruits for dealing with these issues, and the Feltus lab is at the forefront of this technology wave resulting in improvement to the Lab's core biological research mission. Key fruits being harvested:

-Optimized next-generation sequencing (NGS) analysis workflows. Points of optimization include software-defined networking control of bulk data transfers, remote memory data access, recoding algorithms into faster languages (e.g. Perl to C), algorithm modification to a MapReduce paradigm, and porting algorithms to GPUs. For example, we ported gene expression matrix construction to the Open Science Grid [7]. In collaboration with Indiana University and LSU, we are involved with the construction of sequence object based distributed parallel runtime environment for NGS processing based on HPX. Funding support: "BIGDATA: F: DKM: Collaborative Research: PXFS: ParalleX Based Transformative I/O System for Big Data" NSF-BIGDATA Award #1447771, $720,000. Finally, we have a $2.9 million NSF CC* proposal pending entitled: "National Cyberinfrastructure for Scientific Data Analysis at Scale (SciDAS)" (Feltus PI).

-Fast Biological Network Construction and Analysis. We have optimized network construction software that dramatically reduces processing time (e.g. github.com/spficklin/RMTGeneNet). We are also polishing new algorithms for network construction that run on the Open Science Grid and we have applied these algorithms to The Cancer Genome Atlas dataset (manuscript in preparation). This research is in heavy collaboration with Stephen Ficklin (WSU), Melissa Smith (CU), and Karan Sapra (nVIDIA).

-Bulk Data Transfers. We are working on software defined networking control mechanisms and are testing parallel data transfers between endpoints at Clemson, Washington State, Tennessee, Connecticut, Utah and NCBI. We have engineered data transfer abstraction software that plugs into Galaxy and works as a standalone client called the Big Data Smart Socket (BDSS) for optimal data transfers ([8]; https://github.com/feltus/BDSS). These activities are helping us identify optimal methods for streaming parallel big data flows across advanced networks onto parallel filesystems, a severe workflow bottleneck (e.g. [9]). Funding support: "Tripal Gateway: Platform for Next-Generation Data Analysis and Sharing" (NSF-DIBBS Award #1443040, $1,485,021).

-Bionetwork Visualization. We have found that existing network visualization tools like Cytoscape do not meet our high dimensional demand, so we have engineered Biological Dependency Visualizer software (BioDep-Vis; submitted) which is a fully functional interaction framework built using CUDA and OpenGL for nVIDIA GPUs. BioDep-Vis was developed with M. Smith and K. Sapra and is currently available on the Palmetto Cluster. Core features on BioDep-vis include gene expression matrix distribution and biograph visualization, GPU calculated force directed layout of biographs, ontology mappings to nodes, and molecular structure visualization. Experiments are configured using a Python-Qt configuration generator front end that by user-defined data and metadata from local flat files. A key feature is that the software allows for the detection of conserved subgraphs via an nVIDIA CUDA/GPU-enabled graph alignment package we developed called G3NA that aligns two gene interaction networks based upon shared node sequence homology and topology (under review; available at network.genome.clemson.edu). G3NA is an ultrafast algorithm and that detects conserved gene patterns in seconds instead of hours.

-Big Data Leadership. Feltus is co-chair of the Internet2 Distributed Big Data & Analytics working group and member of the Internet2 CINO Advisory Board. Feltus is a key liaison between the NSF funded South Big Data Hub and is the faculty chair of CU-CAT, a Clemson University wide research computing governance committee that reports to the CIO.

 Extension and Outreach

Dr. F. Alex Feltus is developing systems genetics tools for SC plant breeders.

 Publications

(>2008)
1. Hannah Schmucker, Jang Pyo Park, Marie-May Coissieux, Kerri Kwist, Mohamed Bentires-Alj, F. Alex Feltus, and Brian W. Booth. “RNA expression profiling reveal differentially regulated growth factor and receptor expression in redirected cancer cells." Stem Cells and Development (in press), 2017.
2. Nick A. Watts and Frank A. Feltus. "Big Data Smart Socket (BDSS): A Tool that Abstracts Data Transfer Habits from End Users." Bioinformatics in press, 2016.
3. Nicholas Mills, F. Alex Feltus, Walter B. Ligon III. "Maximizing the Performance of Scientific Data Transfer by Optimizing the Interface Between Parallel File Systems and Advanced Research Networks" Future Generation Computer Systems. in press, 2016.
4. William L. Poehlman, Mats Rynge, Chris Branton, D. Balamurugan, and Frank A. Feltus. "OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid." Bioinformatics and Biology Insights 10:133, 2016. TC#6455.
5. Yupeng Wang, Stephen P. Ficklin, Xiyin Wang, Frank A. Feltus, Andrew H. Paterson. “Large-scale gene relocations following an ancient genome triplication associated with the diversification of core eudicots.” PLOS ONE (in press), 2016.
6. Frank A. Feltus, Joe Breen, Juan Deng, Ryan Izard, Christopher A Konger, Walt Ligon, Don Preuss, Kuangching Wang. The Widening Gulf Between Genomics Data Generation and Consumption- A Practical Guide To Big Data Transfer Technology. Bioinformatics and Biology Insights Suppl. 1 9-19, 2015.
7. Clyde Phelix and F. Alex Feltus. Plant Stress Biomarkers from Biosimulations: The Transcriptome-To-Metabolometm (TTMtm) Technology. Effects of drought stress on rice. Plant Biology Plant Biology 17 (1), 63-73, 2015.
8. Feltus FA Systems Genetics: A Paradigm to Improve Discovery of Candidate Genes and Mechanisms Underlying Complex Traits. Plant Science 223, 45-48, 2014.
9. Roger N. Hilten, Joshua P. Vandenbrink, Andrew H. Paterson, F. Alex Feltus, and Keshav C. Das. Linking isoconversional pyrolysis kinetics to compositional characteristics for multiple Sorghum bicolor genotypes. Thermochimica Acta 577, 46-52, 2014. TC#6176.
10. Yannick Pauchet, Christopher A. Saski, Frank A. Feltus, Isabelle Luyten, Hadi Quesneville, and David G. Heckel. Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremulae provides insights into a leaf beetle genome. Insect Molecular Biology 23(3):286-300, 2014.
11. Nadia Shakoor, Ramesh Nair, Oswald Crasta, Geoffrey Morris, Alex Feltus and Stephen Kresovich A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC Plant Biology 14(1):35, 2014.
12. Sanderson LA, Ficklin SP, Cheng CH, Jung S, Bett KE, Feltus FA, Main D Tripal 1.1: a Standards-based Platform for Construction of Online Genetic, Genomic and Biological Databases. Database (Oxford) doi: 10.1093/database/bat075, 2013.
13. Joshua P. Vandenbrink, Ryan E Hammonds, Andrew H. Paterson, KC Das, J Michael Henson, Roger N. Hilten, and F. Alex Feltus. Tissue specific analysis of hydrolysis related traits and pretreatment efficacy in the bioenergy grass Sorghum bicolor. Industrial Crops & Products 50:118-130, 2013. TC#6018.
14. Joshua P. Vandenbrink, Andrew H. Paterson, Lori Goff, Wenqian Kong, Huizhe Jin and F. Alex Feltus. Identification of Bioconversion Quantitative Trait Loci in the Interspecific Bioenergy Grass Cross Sorghum bicolor x Sorghum propinquum. Theoretical and Applied Genetics 126(9):2367-80, 2013. TC#6096.
15. Stephen P. Ficklin and F. Alex Feltus. A Systems-Genetics Approach and Data Mining Tool For the Discovery of Genes Underlying Complex Traits in Oryza Sativa. PloS ONE 8(7): e68551, 2013.
16. F. Alex Feltus, Stephen P. Ficklin, Scott M Gibson, and Melissa C. Smith. Maximizing Capture of Gene Co-expression Relationships Through Pre-Clustering of Input Expression Samples: An Arabidopsis Case Study. BMC Systems Biology 7:44, doi:10.1186/1752-0509-7-44, 2013
17. Jacob B Spangler and F. Alex Feltus. Conserved Noncoding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. Frontiers in Plant Science. doi:10.3389/fpls.2013.00129, 2013.
18. Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida and David N Kuhn. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology 14(6):R53 doi:10.1186/gb-2013-14-6-r532013, 2013.
19. Joshua P. Vandenbrink, Andrew H. Paterson, KC Das, Roger N. Hilten, and F. Alex Feltus. Quantitative Models of Hydrolysis Conversion Efficiency and Biomass Crystallinity Index for Plant Breeding. Plant Breeding, 132(3): 252–258, 2013. TC#6060.
20. Scott M. Gibson, Stephen P. Ficklin, Sven Isaacson, Feng Luo, F. Alex Feltus, Melissa C. Smith. Massive-Scale Gene Co-expression Network Construction and Robustness Testing using Random Matrix Theory. PLoS ONE (2), e55871, 2013.
21. F. Alex Feltus and Joshua P. Vandenbrink. Bioenergy Grass Feedstock: Current options and prospects for improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnology for Biofuels Nov 2;5(1):80, 2012. TC#6038.
22. Jacob B. Spangler, Stephen P. Ficklin, Feng Luo, Michael Freeling and F. Alex Feltus. Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-expressed Gene Modules. PLoS ONE 7(9): e45041. doi:10.1371/journal.pone.0045041, 2012.
23. Jianping Wang, Jong-Kuk Na, Qingyi Yu, Andrea Gschwend, Jennifer Han, Fanchang Zeng, Rishi Aryal, Robert VanBuren, Jan E. Murray, Wenli Zhang, Rafael Navajas Pérez, F. Alex Feltus, Cornelia Lemke, Eric J. Tong, Cuixia Chen, Ching Man Wai, Ratnesh Singh, Ming-Li Wang, Xiangjia Min, Maqsudul Alam, Deborah Charlesworth, Paul H. Moore, Jiming Jiang, Andrew H. Paterson, Ray Ming. Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proceedings of the National Academy of Sciences USA, Aug 21;109(34):13710-5, 2012.
24. Jong-Kuk Na, Jianping Wang, Jan E Murray, Andrea R Gschwend, Wenli Zhang, Qingyi Yu, Rafael N Pérez, F. Alex Feltus, Cuixia Chen, Zdenek Kubat, Paul H Moore, Jiming Jiang, Andrew H Paterson and Ray Ming. Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics, 13:176, 2012.
25. Spangler, Jacob; Subramaniam, Sabarinath; Freeling, Michael, and F. Alex Feltus. Evidence of Function for Conserved Non-coding Sequence in Arabidopsis thaliana. New Phytologist, 193(1):241-252, 2012.
26. Yupeng Wang, Xiyin Wang, Haibao Tang, Xu Tan, Stephen Ficklin, F. Alex Feltus and Andrew H Paterson. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS ONE, 6(12): e28150, 2011.
27. David N. Kuhn, Don Livingstone III, Dorrie Main, Ping Zheng, Chris Saski, F. Alex Feltus, Keithanne Mockaitis, Andrew D. Farmer, Gregory D. May, Raymond J. Schnell, and Juan C. Motamayor. Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies. Tree Genetics & Genomes, 8(1):97-111, 2012.
28. Joshua P. Vandenbrink, Roger N. Hilten, K.C. Das, Andrew H. Paterson, and F. Alex Feltus. Analysis of Crystallinity Index and Hydrolysis Rates in the Bioenergy Crop Sorghum bicolor. BioEnergy Research, 5(2):387-397, 2012. TC#5906.
29. Christopher A. Saski, Frank A Feltus, Margaret E Staton, Barbara P Blackmon, Stephen P Ficklin, David N Kuhn, Ray Schnell, Howard Shapiro, Juan Carlos Motamayor. A genetically anchored physical framework for Theobroma cacao (cv. Matina 1-6). BMC Genomics. 12:413, 2011.
30. Frank A. Feltus, Chris A. Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E. Staton, Stephen P. Ficklin, Barbara P. Blackmon, Ray J. Schnell, David N. Kuhn, Juan-Carlos Motamayor. Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes. BMC Genomics, 12(1):379, 2011.
31. Christopher A. Saski, Zhigang Li, Frank A. Feltus, Hong Luo. New genomic resources for switchgrass: a bacterial artificial chromosome library (BAC) and comparative analysis of a homoeologous genomic region harboring bioenergy traits. BMC Genomics, 12:369, 2011.
32. Xumeng Li, F. Alex Feltus, Xiaoqian Sun, Zijun Wang and Feng Luo. Identifying Differentially Expressed Genes in Cancer Patients using A Non-parameter Ising Model. Proteomics, 11(19):3845-52, 2011.
33. Stephen P. Ficklin and F. Alex Feltus. Gene Co-Expression Network Alignment and Conservation of Gene Modules Between Two Grass Species: Maize (Zea mays) and Rice (Oryza sativa). Plant Physiology 156(3):1244-56, 2011.
34. Niina Haiminen, F. Alex Feltus, Laxmi Parida. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Assembly of Complex Genomes. BMC Genomics 12:194, 2011.
35. Stephen P. Ficklin, Feng Luo, and F. Alex Feltus. The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks. Plant Physiology 154(1):13-24, 2010.
36. Mahendar Thudi, Senapathi Senthilvel, Andrew Bottley, C. Tom Hash, Arjula R. Reddy, Alex Feltus, Andrew H. Paterson, David A. Hoisington, Rajeev K. Varshney. A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica 174(2):253-260, 2010.
37. Joshua P. Vandenbrink, Maria P. Delgado, Jim R. Frederick, and F. Alex Feltus. A Sorghum Diversity Panel Biofuel Feedstock Screen for Genotypes with High Hydrolysis Yield Potential. Industrial Crops and Products 31(3):444-448, 2010. TC#5759.
38. Xumeng Li, F. Alex Feltus, Xiaoqian Sun, Zijun Wang, and Feng Luo. A Non-parameter Ising Model for Network-based Identification of Differentially Expressed Genes in Recurrent Breast Cancer Patients. IEEE International Conference on Bioinformatics and Biomedicine (18-21):214-217, 2010.
39. Junkang Rong, Frank A. Feltus, Limei Liu, Lifeng Lin, Andrew H. Paterson. Gene copy number evolution during tetraploid cotton radiation. Heredity 105:463–472, 2010.
40. Shin Sato, F. Alex Feltus, Prashanti Iyer, and Ming Tien. The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak. Current Genetics. 55(3):273-86, 2009. TC#5685.
41. J. A. Buggs, N. Doust, R., J. A. Tate, J. Koh, K. Soltis, F. A. Feltus, A. H. Paterson, P. S. Soltis, D. E. Soltis. Gene Loss and Silencing in Tragopogon miscellus (Asteraceae): Comparison of Natural and Synthetic Allotetraploids. Heredity. (1) 1-9, 2009.
42. Andrew H. Paterson, John E. Bowers, Remy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Uffe Hellsten, Therese Mitros, Alexander Poliakov, Jeremy Schmutz, Manuel Spannagl, Haibao Tang, Xiyin Wang, Thomas Wicker, Arvind K. Bharti, Jarrod Chapman, F. Alex Feltus, Udo Gowik, Eric Lyons, Christopher Maher, Mihaela Martis, Apurva Narechania, Bryan Penning, Yu Wang, Lifang Zhang, Nicholas C. Carpita, Michael Freeling, Alan R. Gingle, C. Thomas Hash, Beat Keller, Patricia Klein, Stephen Kresovich, Maureen C. McCann, Ray Ming, Daniel G. Peterson, Mehboob ur-Rahman, Doreen Ware, Peter Westhoff, Klaus F.X. Mayer, Joachim Messing, Daniel S. Rokhsar. The Sorghum bicolor genome and the diversification of grasses. Nature. 457(7229):551-6, 2009.
43. Ksenija Gasic, Delkin Gonzalez, Jyothi Thimmapuram, Mickael Malnoy, George Gong, Yuepeng Han, Lila O Vodkin, Lei Liu, Herb S Aldwinckle, Natalie J Carroll, Kathryn S Orvis, Peter Goldsbrough, Sandra Clifton, Deana Pape, Lucinda Fulton, John Martin, Brenda Theising, Michael E. Wisniewski, Gennaro Fazio, F. Alex Feltus, Schuyler S Korban. Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple. The Plant Genome. (2)23–38, 2009.
44. Andrew H. Paterson, John E. Bowers, Frank A. Feltus, Haibao Tang, Xiyin Wang. Comparative genomics of the grasses: Promising a bountiful harvest. Plant Physiology 149(1):125-31, Jan. 2009.
45. (BOOK) Saski CA, Feltus FA, Parida L, Haiminen N. "BAC Sequencing Using Pooled Methods." Methods in Molecular Biology. 2015 (in press)
46. (BOOK) Milton Yutaka Nishiyama-Jr, Fabio Vicente, Paloma Mieko Sato, Savio Siqueira Ferreira, Frank Alex Feltus and Glaucia M Souza. The Saccharinae transcriptome. In Plant Genetics and Genomics: Crops and Models, Vol. 11: Genetics and Genomics of the Saccharinae. Paterson, Andrew H. (Ed). Springer, New York. 2013. ISBN: 978-1-4419-5946-1.
47. (BOOK) A Gingle and FA Feltus. Saccharinae bioinformatics resources. in Genomics of the Saccharinae. In Plant Genetics and Genomics: Crops and Models, Vol. 11: Genetics and Genomics of the Saccharinae. Paterson, Andrew H. (Ed). Springer, New York. 2013. ISBN: 978-1-4419-5946-1.
48. (TECHNCAL PAPER) Dmitriy Beloslyudtsev, Dmitry Bulgakov, Joseph Bernard, Mike Cannon, Edward B. Duffy, Frank A. Feltus*, Corey Ferrier, Frank Gao, Christopher A Konger, Blaine Lee, Yang Li, Kathryn Mace, Dierdre Odom, Brian Parker, Jim Pepin, Don Preuss, Robert Schwartzkopf, Kuangching Wang. Configuring a 100Gbit Internet2 Connection Between Two Institutions: Practical Advice and Prospects. Internet2 Case Study. http://www.internet2.edu/research-solutions/case-studies/accelerating-genomic-research-advanced-networking-collaborations (August 2014).
49. (TECHNCAL PAPER) Bo Li, James Z. Wang, F. Alex Feltus, Feng Luo. Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins. BIOCOMP'10 Conference Proceedings (July 12, 2010).

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Genetics & Biochemistry Department
Clemson Computational Advisory Team (CU-CAT)
Internet2 Distributed Big Data & Analytics Working Group